Ben Bolstad
| Snapshot Date: 2026-04-03 13:45 -0400 (Fri, 03 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/BufferedMatrix |
| git_branch: RELEASE_3_22 |
| git_last_commit: d2ce144 |
| git_last_commit_date: 2025-10-29 09:58:55 -0400 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.22: simplified long |
|
This page was generated on 2026-04-04 11:57 -0400 (Sat, 04 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4897 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 257/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| BufferedMatrix 1.74.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| See other builds for BufferedMatrix in R Universe. | ||||||||||||||
|
To the developers/maintainers of the BufferedMatrix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BufferedMatrix.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: BufferedMatrix |
| Version: 1.74.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz |
| StartedAt: 2026-04-03 21:35:18 -0400 (Fri, 03 Apr 2026) |
| EndedAt: 2026-04-03 21:35:42 -0400 (Fri, 03 Apr 2026) |
| EllapsedTime: 24.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: BufferedMatrix.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:BufferedMatrix.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings BufferedMatrix_1.74.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck’
* using R version 4.5.2 (2025-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BufferedMatrix/DESCRIPTION’ ... OK
* this is package ‘BufferedMatrix’ version ‘1.74.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BufferedMatrix’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... NOTE
checkRd: (-1) BufferedMatrix-class.Rd:209: Lost braces; missing escapes or markup?
209 | $x^{power}$ elementwise of the matrix
| ^
prepare_Rd: createBufferedMatrix.Rd:26: Dropping empty section \keyword
prepare_Rd: createBufferedMatrix.Rd:17-18: Dropping empty section \details
prepare_Rd: createBufferedMatrix.Rd:15-16: Dropping empty section \value
prepare_Rd: createBufferedMatrix.Rd:19-20: Dropping empty section \references
prepare_Rd: createBufferedMatrix.Rd:21-22: Dropping empty section \seealso
prepare_Rd: createBufferedMatrix.Rd:23-24: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘Rcodetesting.R’
Running ‘c_code_level_tests.R’
Running ‘objectTesting.R’
Running ‘rawCalltesting.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/00check.log’
for details.
BufferedMatrix.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL BufferedMatrix
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘BufferedMatrix’ ...
** this is package ‘BufferedMatrix’ version ‘1.74.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RBufferedMatrix.c -o RBufferedMatrix.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix.c -o doubleBufferedMatrix.o
doubleBufferedMatrix.c: In function ‘dbm_ReadOnlyMode’:
doubleBufferedMatrix.c:1580:7: warning: suggest parentheses around operand of ‘!’ or change ‘&’ to ‘&&’ or ‘!’ to ‘~’ [-Wparentheses]
1580 | if (!(Matrix->readonly) & setting){
| ^~~~~~~~~~~~~~~~~~~
doubleBufferedMatrix.c: At top level:
doubleBufferedMatrix.c:3327:12: warning: ‘sort_double’ defined but not used [-Wunused-function]
3327 | static int sort_double(const double *a1,const double *a2){
| ^~~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c doubleBufferedMatrix_C_tests.c -o doubleBufferedMatrix_C_tests.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c init_package.c -o init_package.o
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/lib -o BufferedMatrix.so RBufferedMatrix.o doubleBufferedMatrix.o doubleBufferedMatrix_C_tests.o init_package.o -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-BufferedMatrix/00new/BufferedMatrix/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘rowMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘rowSums’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colMeans’ in package ‘BufferedMatrix’
Creating a new generic function for ‘colSums’ in package ‘BufferedMatrix’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘BufferedMatrix’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘BufferedMatrix’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BufferedMatrix)
BufferedMatrix.Rcheck/tests/c_code_level_tests.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix", "BufferedMatrix", .libPaths());.C("dbm_c_tester",integer(1))
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
Adding Additional Column
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000
Reassigning values
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 3
Buffer Cols: 3
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Activating Row Buffer
In row mode: 1
1.000000 6.000000 11.000000 16.000000 21.000000 26.000000
2.000000 7.000000 12.000000 17.000000 22.000000 27.000000
3.000000 8.000000 13.000000 18.000000 23.000000 28.000000
4.000000 9.000000 14.000000 19.000000 24.000000 29.000000
5.000000 10.000000 15.000000 20.000000 25.000000 30.000000
Squaring Last Column
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
5.000000 10.000000 15.000000 20.000000 25.000000 900.000000
Square rooting Last Row, then turing off Row Buffer
In row mode: 0
Checking on value that should be not be in column buffer2.236068
1.000000 6.000000 11.000000 16.000000 21.000000 676.000000
2.000000 7.000000 12.000000 17.000000 22.000000 729.000000
3.000000 8.000000 13.000000 18.000000 23.000000 784.000000
4.000000 9.000000 14.000000 19.000000 24.000000 841.000000
2.236068 3.162278 3.872983 4.472136 5.000000 30.000000
Single Indexing. Assign each value its square
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Resizing Buffers Smaller
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
1.000000 36.000000 121.000000 256.000000 441.000000 676.000000
4.000000 49.000000 144.000000 289.000000 484.000000 729.000000
9.000000 64.000000 169.000000 324.000000 529.000000 784.000000
16.000000 81.000000 196.000000 361.000000 576.000000 841.000000
25.000000 100.000000 225.000000 400.000000 625.000000 900.000000
Activating Row Mode.
Resizing Buffers
Checking dimensions
Rows: 5
Cols: 6
Buffer Rows: 1
Buffer Cols: 1
Activating ReadOnly Mode.
The results of assignment is: 0
Printing matrix reversed.
900.000000 625.000000 400.000000 225.000000 100.000000 25.000000
841.000000 576.000000 361.000000 196.000000 81.000000 16.000000
784.000000 529.000000 324.000000 169.000000 64.000000 9.000000
729.000000 484.000000 289.000000 144.000000 49.000000 -30.000000
676.000000 441.000000 256.000000 121.000000 -20.000000 -10.000000
[[1]]
[1] 0
>
> proc.time()
user system elapsed
0.247 0.038 0.276
BufferedMatrix.Rcheck/tests/objectTesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
>
> ### this is used to control how many repetitions in something below
> ### higher values result in more checks.
> nreps <-100 ##20000
>
>
> ## test creation and some simple assignments and subsetting operations
>
> ## first on single elements
> tmp <- createBufferedMatrix(1000,10)
>
> tmp[10,5]
[1] 0
> tmp[10,5] <- 10
> tmp[10,5]
[1] 10
> tmp[10,5] <- 12.445
> tmp[10,5]
[1] 12.445
>
>
>
> ## now testing accessing multiple elements
> tmp2 <- createBufferedMatrix(10,20)
>
>
> tmp2[3,1] <- 51.34
> tmp2[9,2] <- 9.87654
> tmp2[,1:2]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[,-(3:20)]
[,1] [,2]
[1,] 0.00 0.00000
[2,] 0.00 0.00000
[3,] 51.34 0.00000
[4,] 0.00 0.00000
[5,] 0.00 0.00000
[6,] 0.00 0.00000
[7,] 0.00 0.00000
[8,] 0.00 0.00000
[9,] 0.00 9.87654
[10,] 0.00 0.00000
> tmp2[3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 51.34 0 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
> tmp2[-3,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19] [,20]
[1,] 0 0 0 0 0 0 0
[2,] 0 0 0 0 0 0 0
[3,] 0 0 0 0 0 0 0
[4,] 0 0 0 0 0 0 0
[5,] 0 0 0 0 0 0 0
[6,] 0 0 0 0 0 0 0
[7,] 0 0 0 0 0 0 0
[8,] 0 0 0 0 0 0 0
[9,] 0 0 0 0 0 0 0
> tmp2[2,1:3]
[,1] [,2] [,3]
[1,] 0 0 0
> tmp2[3:9,1:3]
[,1] [,2] [,3]
[1,] 51.34 0.00000 0
[2,] 0.00 0.00000 0
[3,] 0.00 0.00000 0
[4,] 0.00 0.00000 0
[5,] 0.00 0.00000 0
[6,] 0.00 0.00000 0
[7,] 0.00 9.87654 0
> tmp2[-4,-4]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[2,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[3,] 51.34 0.00000 0 0 0 0 0 0 0 0 0 0 0
[4,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[5,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[6,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[7,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[8,] 0.00 9.87654 0 0 0 0 0 0 0 0 0 0 0
[9,] 0.00 0.00000 0 0 0 0 0 0 0 0 0 0 0
[,14] [,15] [,16] [,17] [,18] [,19]
[1,] 0 0 0 0 0 0
[2,] 0 0 0 0 0 0
[3,] 0 0 0 0 0 0
[4,] 0 0 0 0 0 0
[5,] 0 0 0 0 0 0
[6,] 0 0 0 0 0 0
[7,] 0 0 0 0 0 0
[8,] 0 0 0 0 0 0
[9,] 0 0 0 0 0 0
>
> ## now testing accessing/assigning multiple elements
> tmp3 <- createBufferedMatrix(10,10)
>
> for (i in 1:10){
+ for (j in 1:10){
+ tmp3[i,j] <- (j-1)*10 + i
+ }
+ }
>
> tmp3[2:4,2:4]
[,1] [,2] [,3]
[1,] 12 22 32
[2,] 13 23 33
[3,] 14 24 34
> tmp3[c(-10),c(2:4,2:4,10,1,2,1:10,10:1)]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
[1,] 11 21 31 11 21 31 91 1 11 1 11 21 31
[2,] 12 22 32 12 22 32 92 2 12 2 12 22 32
[3,] 13 23 33 13 23 33 93 3 13 3 13 23 33
[4,] 14 24 34 14 24 34 94 4 14 4 14 24 34
[5,] 15 25 35 15 25 35 95 5 15 5 15 25 35
[6,] 16 26 36 16 26 36 96 6 16 6 16 26 36
[7,] 17 27 37 17 27 37 97 7 17 7 17 27 37
[8,] 18 28 38 18 28 38 98 8 18 8 18 28 38
[9,] 19 29 39 19 29 39 99 9 19 9 19 29 39
[,14] [,15] [,16] [,17] [,18] [,19] [,20] [,21] [,22] [,23] [,24] [,25]
[1,] 41 51 61 71 81 91 91 81 71 61 51 41
[2,] 42 52 62 72 82 92 92 82 72 62 52 42
[3,] 43 53 63 73 83 93 93 83 73 63 53 43
[4,] 44 54 64 74 84 94 94 84 74 64 54 44
[5,] 45 55 65 75 85 95 95 85 75 65 55 45
[6,] 46 56 66 76 86 96 96 86 76 66 56 46
[7,] 47 57 67 77 87 97 97 87 77 67 57 47
[8,] 48 58 68 78 88 98 98 88 78 68 58 48
[9,] 49 59 69 79 89 99 99 89 79 69 59 49
[,26] [,27] [,28] [,29]
[1,] 31 21 11 1
[2,] 32 22 12 2
[3,] 33 23 13 3
[4,] 34 24 14 4
[5,] 35 25 15 5
[6,] 36 26 16 6
[7,] 37 27 17 7
[8,] 38 28 18 8
[9,] 39 29 19 9
> tmp3[-c(1:5),-c(6:10)]
[,1] [,2] [,3] [,4] [,5]
[1,] 6 16 26 36 46
[2,] 7 17 27 37 47
[3,] 8 18 28 38 48
[4,] 9 19 29 39 49
[5,] 10 20 30 40 50
>
> ## assignment of whole columns
> tmp3[,1] <- c(1:10*100.0)
> tmp3[,1:2] <- tmp3[,1:2]*100
> tmp3[,1:2] <- tmp3[,2:1]
> tmp3[,1:2]
[,1] [,2]
[1,] 1100 1e+04
[2,] 1200 2e+04
[3,] 1300 3e+04
[4,] 1400 4e+04
[5,] 1500 5e+04
[6,] 1600 6e+04
[7,] 1700 7e+04
[8,] 1800 8e+04
[9,] 1900 9e+04
[10,] 2000 1e+05
>
>
> tmp3[,-1] <- tmp3[,1:9]
> tmp3[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1100 1100 1e+04 21 31 41 51 61 71 81
[2,] 1200 1200 2e+04 22 32 42 52 62 72 82
[3,] 1300 1300 3e+04 23 33 43 53 63 73 83
[4,] 1400 1400 4e+04 24 34 44 54 64 74 84
[5,] 1500 1500 5e+04 25 35 45 55 65 75 85
[6,] 1600 1600 6e+04 26 36 46 56 66 76 86
[7,] 1700 1700 7e+04 27 37 47 57 67 77 87
[8,] 1800 1800 8e+04 28 38 48 58 68 78 88
[9,] 1900 1900 9e+04 29 39 49 59 69 79 89
[10,] 2000 2000 1e+05 30 40 50 60 70 80 90
>
> tmp3[,1:2] <- rep(1,10)
> tmp3[,1:2] <- rep(1,20)
> tmp3[,1:2] <- matrix(c(1:5),1,5)
>
> tmp3[,-c(1:8)] <- matrix(c(1:5),1,5)
>
> tmp3[1,] <- 1:10
> tmp3[1,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
> tmp3[-1,] <- c(1,2)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 2 1 2 1 2 1 2 1 2 1
[10,] 1 2 1 2 1 2 1 2 1 2
> tmp3[-c(1:8),] <- matrix(c(1:5),1,5)
> tmp3[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 1 2 3 4 5 6 7 8 9 10
[2,] 1 2 1 2 1 2 1 2 1 2
[3,] 2 1 2 1 2 1 2 1 2 1
[4,] 1 2 1 2 1 2 1 2 1 2
[5,] 2 1 2 1 2 1 2 1 2 1
[6,] 1 2 1 2 1 2 1 2 1 2
[7,] 2 1 2 1 2 1 2 1 2 1
[8,] 1 2 1 2 1 2 1 2 1 2
[9,] 1 3 5 2 4 1 3 5 2 4
[10,] 2 4 1 3 5 2 4 1 3 5
>
>
> tmp3[1:2,1:2] <- 5555.04
> tmp3[-(1:2),1:2] <- 1234.56789
>
>
>
> ## testing accessors for the directory and prefix
> directory(tmp3)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests"
> prefix(tmp3)
[1] "BM"
>
> ## testing if we can remove these objects
> rm(tmp, tmp2, tmp3)
> gc()
used (Mb) gc trigger (Mb) max used (Mb)
Ncells 478284 25.6 1046725 56 639600 34.2
Vcells 884773 6.8 8388608 64 2081613 15.9
>
>
>
>
> ##
> ## checking reads
> ##
>
> tmp2 <- createBufferedMatrix(10,20)
>
> test.sample <- rnorm(10*20)
>
> tmp2[1:10,1:20] <- test.sample
>
> test.matrix <- matrix(test.sample,10,20)
>
> ## testing reads
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Fri Apr 3 21:35:33 2026"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Fri Apr 3 21:35:33 2026"
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
>
>
> RowMode(tmp2)
<pointer: 0x58f12751d1c0>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ which.col <- sample(1:20,1)
+ if (tmp2[which.row,which.col] != test.matrix[which.row,which.col]){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[,which.col] == test.matrix[,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ if (!all(tmp2[which.row,] == test.matrix[which.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
>
>
> date()
[1] "Fri Apr 3 21:35:34 2026"
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ if (!all(tmp2[which.row,which.col] == test.matrix[which.row,which.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
> date()
[1] "Fri Apr 3 21:35:34 2026"
>
> ColMode(tmp2)
<pointer: 0x58f12751d1c0>
>
>
>
> ### Now testing assignments
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,1)
+
+ new.data <- rnorm(20)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,] <- new.data
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,1)
+ new.data <- rnorm(10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[,which.col] <- new.data
+ test.matrix[,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[,prev.col] == test.matrix[,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.col <- which.col
+ }
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ new.data <- matrix(rnorm(50),5,10)
+ tmp2[which.row,] <- new.data
+ test.matrix[which.row,]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,] == test.matrix[prev.row,])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ }
>
>
>
>
>
> for (rep in 1:nreps){
+ which.row <- sample(1:10,5,replace=TRUE)
+ which.col <- sample(1:20,5,replace=TRUE)
+ new.data <- matrix(rnorm(25),5,5)
+ tmp2[which.row,which.col] <- new.data
+ test.matrix[which.row,which.col]<- new.data
+
+ if (rep > 1){
+ if (!all(tmp2[prev.row,prev.col] == test.matrix[prev.row,prev.col])){
+ cat("incorrect agreement")
+ break;
+ }
+ }
+ prev.row <- which.row
+ prev.col <- which.col
+ }
>
>
>
>
> ###
> ###
> ### testing some more functions
> ###
>
>
>
> ## duplication function
> tmp5 <- duplicate(tmp2)
>
> # making sure really did copy everything.
> tmp5[1,1] <- tmp5[1,1] +100.00
>
> if (tmp5[1,1] == tmp2[1,1]){
+ stop("Problem with duplication")
+ }
>
>
>
>
> ### testing elementwise applying of functions
>
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 98.6509750 0.2034275 0.9536659 -0.1744629
[2,] 0.9840820 0.8120968 -0.2997725 0.4560195
[3,] 0.3641736 -0.3661409 0.6429093 -0.2693986
[4,] 1.1005297 -1.0008869 1.6690506 -0.3101617
> ewApply(tmp5,abs)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 98.6509750 0.2034275 0.9536659 0.1744629
[2,] 0.9840820 0.8120968 0.2997725 0.4560195
[3,] 0.3641736 0.3661409 0.6429093 0.2693986
[4,] 1.1005297 1.0008869 1.6690506 0.3101617
> ewApply(tmp5,sqrt)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 9.9323197 0.4510294 0.9765582 0.4176875
[2,] 0.9920091 0.9011641 0.5475149 0.6752922
[3,] 0.6034680 0.6050958 0.8018162 0.5190362
[4,] 1.0490614 1.0004433 1.2919174 0.5569216
>
> my.function <- function(x,power){
+ (x+5)^power
+ }
>
> ewApply(tmp5,my.function,power=2)
BufferedMatrix object
Matrix size: 10 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 1.6 Kilobytes.
> tmp5[1:4,1:4]
[,1] [,2] [,3] [,4]
[1,] 222.97417 29.71372 35.71925 29.35134
[2,] 35.90417 34.82374 30.77492 32.20894
[3,] 31.39885 31.41710 33.66107 30.45976
[4,] 36.59114 36.00532 39.58822 30.87938
>
>
>
> ## testing functions that elementwise transform the matrix
> sqrt(tmp5)
<pointer: 0x58f1281238b0>
> exp(tmp5)
<pointer: 0x58f1281238b0>
> log(tmp5,2)
<pointer: 0x58f1281238b0>
> pow(tmp5,2)
>
>
>
>
>
> ## testing functions that apply to entire matrix
> Max(tmp5)
[1] 464.0915
> Min(tmp5)
[1] 53.75548
> mean(tmp5)
[1] 73.51978
> Sum(tmp5)
[1] 14703.96
> Var(tmp5)
[1] 841.7246
>
>
> ## testing functions applied to rows or columns
>
> rowMeans(tmp5)
[1] 88.31622 72.28859 72.61719 71.30100 72.80312 70.43651 71.04884 70.48685
[9] 74.68566 71.21385
> rowSums(tmp5)
[1] 1766.324 1445.772 1452.344 1426.020 1456.062 1408.730 1420.977 1409.737
[9] 1493.713 1424.277
> rowVars(tmp5)
[1] 7875.71059 94.21798 78.25636 36.29137 79.66910 66.37717
[7] 75.59537 105.41909 78.12484 54.51813
> rowSd(tmp5)
[1] 88.745200 9.706595 8.846262 6.024232 8.925755 8.147218 8.694560
[8] 10.267380 8.838826 7.383639
> rowMax(tmp5)
[1] 464.09153 90.81793 90.96510 82.39770 91.49576 87.30004 86.49421
[8] 88.12020 92.43885 83.76616
> rowMin(tmp5)
[1] 56.06291 53.75548 60.53412 61.28409 57.60986 55.08755 55.65290 56.52651
[9] 61.63894 56.70492
>
> colMeans(tmp5)
[1] 110.87886 68.31180 70.98173 68.27239 71.94665 72.60411 67.12922
[8] 72.93269 71.27713 71.59736 73.02395 74.10693 74.75080 71.71287
[15] 70.74094 68.21505 75.46100 75.16769 72.09233 69.19214
> colSums(tmp5)
[1] 1108.7886 683.1180 709.8173 682.7239 719.4665 726.0411 671.2922
[8] 729.3269 712.7713 715.9736 730.2395 741.0693 747.5080 717.1287
[15] 707.4094 682.1505 754.6100 751.6769 720.9233 691.9214
> colVars(tmp5)
[1] 15440.36477 70.05770 51.14918 27.67309 53.12453 54.27459
[7] 13.38999 125.47112 91.45868 102.91633 111.74138 63.47477
[13] 66.18475 57.96478 103.66226 66.56098 97.48818 118.95719
[19] 27.69834 113.95799
> colSd(tmp5)
[1] 124.259264 8.370048 7.151865 5.260522 7.288657 7.367129
[7] 3.659233 11.201389 9.563403 10.144769 10.570779 7.967106
[13] 8.135401 7.613461 10.181467 8.158491 9.873611 10.906750
[19] 5.262921 10.675111
> colMax(tmp5)
[1] 464.09153 85.14123 82.39770 77.40231 82.11319 90.81793 73.43942
[8] 85.51094 91.05468 88.93336 88.12020 82.78659 87.30004 83.61109
[15] 86.49421 83.30314 90.96510 92.43885 79.62450 83.76616
> colMin(tmp5)
[1] 57.60986 56.52651 61.27379 61.09096 59.94173 65.77545 62.35500 53.75548
[9] 61.73536 57.11269 55.08755 58.91640 62.66511 60.04278 59.82470 56.70492
[17] 62.38349 61.73116 63.45138 56.06291
>
>
> ### setting a random element to NA and then testing with na.rm=TRUE or na.rm=FALSE (The default)
>
>
> which.row <- sample(1:10,1,replace=TRUE)
> which.col <- sample(1:20,1,replace=TRUE)
>
> tmp5[which.row,which.col] <- NA
>
> Max(tmp5)
[1] NA
> Min(tmp5)
[1] NA
> mean(tmp5)
[1] NA
> Sum(tmp5)
[1] NA
> Var(tmp5)
[1] NA
>
> rowMeans(tmp5)
[1] 88.31622 72.28859 72.61719 71.30100 72.80312 70.43651 71.04884 70.48685
[9] NA 71.21385
> rowSums(tmp5)
[1] 1766.324 1445.772 1452.344 1426.020 1456.062 1408.730 1420.977 1409.737
[9] NA 1424.277
> rowVars(tmp5)
[1] 7875.71059 94.21798 78.25636 36.29137 79.66910 66.37717
[7] 75.59537 105.41909 82.46497 54.51813
> rowSd(tmp5)
[1] 88.745200 9.706595 8.846262 6.024232 8.925755 8.147218 8.694560
[8] 10.267380 9.081023 7.383639
> rowMax(tmp5)
[1] 464.09153 90.81793 90.96510 82.39770 91.49576 87.30004 86.49421
[8] 88.12020 NA 83.76616
> rowMin(tmp5)
[1] 56.06291 53.75548 60.53412 61.28409 57.60986 55.08755 55.65290 56.52651
[9] NA 56.70492
>
> colMeans(tmp5)
[1] NA 68.31180 70.98173 68.27239 71.94665 72.60411 67.12922 72.93269
[9] 71.27713 71.59736 73.02395 74.10693 74.75080 71.71287 70.74094 68.21505
[17] 75.46100 75.16769 72.09233 69.19214
> colSums(tmp5)
[1] NA 683.1180 709.8173 682.7239 719.4665 726.0411 671.2922 729.3269
[9] 712.7713 715.9736 730.2395 741.0693 747.5080 717.1287 707.4094 682.1505
[17] 754.6100 751.6769 720.9233 691.9214
> colVars(tmp5)
[1] NA 70.05770 51.14918 27.67309 53.12453 54.27459 13.38999
[8] 125.47112 91.45868 102.91633 111.74138 63.47477 66.18475 57.96478
[15] 103.66226 66.56098 97.48818 118.95719 27.69834 113.95799
> colSd(tmp5)
[1] NA 8.370048 7.151865 5.260522 7.288657 7.367129 3.659233
[8] 11.201389 9.563403 10.144769 10.570779 7.967106 8.135401 7.613461
[15] 10.181467 8.158491 9.873611 10.906750 5.262921 10.675111
> colMax(tmp5)
[1] NA 85.14123 82.39770 77.40231 82.11319 90.81793 73.43942 85.51094
[9] 91.05468 88.93336 88.12020 82.78659 87.30004 83.61109 86.49421 83.30314
[17] 90.96510 92.43885 79.62450 83.76616
> colMin(tmp5)
[1] NA 56.52651 61.27379 61.09096 59.94173 65.77545 62.35500 53.75548
[9] 61.73536 57.11269 55.08755 58.91640 62.66511 60.04278 59.82470 56.70492
[17] 62.38349 61.73116 63.45138 56.06291
>
> Max(tmp5,na.rm=TRUE)
[1] 464.0915
> Min(tmp5,na.rm=TRUE)
[1] 53.75548
> mean(tmp5,na.rm=TRUE)
[1] 73.51417
> Sum(tmp5,na.rm=TRUE)
[1] 14629.32
> Var(tmp5,na.rm=TRUE)
[1] 845.9694
>
> rowMeans(tmp5,na.rm=TRUE)
[1] 88.31622 72.28859 72.61719 71.30100 72.80312 70.43651 71.04884 70.48685
[9] 74.68820 71.21385
> rowSums(tmp5,na.rm=TRUE)
[1] 1766.324 1445.772 1452.344 1426.020 1456.062 1408.730 1420.977 1409.737
[9] 1419.076 1424.277
> rowVars(tmp5,na.rm=TRUE)
[1] 7875.71059 94.21798 78.25636 36.29137 79.66910 66.37717
[7] 75.59537 105.41909 82.46497 54.51813
> rowSd(tmp5,na.rm=TRUE)
[1] 88.745200 9.706595 8.846262 6.024232 8.925755 8.147218 8.694560
[8] 10.267380 9.081023 7.383639
> rowMax(tmp5,na.rm=TRUE)
[1] 464.09153 90.81793 90.96510 82.39770 91.49576 87.30004 86.49421
[8] 88.12020 92.43885 83.76616
> rowMin(tmp5,na.rm=TRUE)
[1] 56.06291 53.75548 60.53412 61.28409 57.60986 55.08755 55.65290 56.52651
[9] 61.63894 56.70492
>
> colMeans(tmp5,na.rm=TRUE)
[1] 114.90569 68.31180 70.98173 68.27239 71.94665 72.60411 67.12922
[8] 72.93269 71.27713 71.59736 73.02395 74.10693 74.75080 71.71287
[15] 70.74094 68.21505 75.46100 75.16769 72.09233 69.19214
> colSums(tmp5,na.rm=TRUE)
[1] 1034.1512 683.1180 709.8173 682.7239 719.4665 726.0411 671.2922
[8] 729.3269 712.7713 715.9736 730.2395 741.0693 747.5080 717.1287
[15] 707.4094 682.1505 754.6100 751.6769 720.9233 691.9214
> colVars(tmp5,na.rm=TRUE)
[1] 17187.98815 70.05770 51.14918 27.67309 53.12453 54.27459
[7] 13.38999 125.47112 91.45868 102.91633 111.74138 63.47477
[13] 66.18475 57.96478 103.66226 66.56098 97.48818 118.95719
[19] 27.69834 113.95799
> colSd(tmp5,na.rm=TRUE)
[1] 131.102968 8.370048 7.151865 5.260522 7.288657 7.367129
[7] 3.659233 11.201389 9.563403 10.144769 10.570779 7.967106
[13] 8.135401 7.613461 10.181467 8.158491 9.873611 10.906750
[19] 5.262921 10.675111
> colMax(tmp5,na.rm=TRUE)
[1] 464.09153 85.14123 82.39770 77.40231 82.11319 90.81793 73.43942
[8] 85.51094 91.05468 88.93336 88.12020 82.78659 87.30004 83.61109
[15] 86.49421 83.30314 90.96510 92.43885 79.62450 83.76616
> colMin(tmp5,na.rm=TRUE)
[1] 57.60986 56.52651 61.27379 61.09096 59.94173 65.77545 62.35500 53.75548
[9] 61.73536 57.11269 55.08755 58.91640 62.66511 60.04278 59.82470 56.70492
[17] 62.38349 61.73116 63.45138 56.06291
>
> # now set an entire row to NA
>
> tmp5[which.row,] <- NA
> rowMeans(tmp5,na.rm=TRUE)
[1] 88.31622 72.28859 72.61719 71.30100 72.80312 70.43651 71.04884 70.48685
[9] NaN 71.21385
> rowSums(tmp5,na.rm=TRUE)
[1] 1766.324 1445.772 1452.344 1426.020 1456.062 1408.730 1420.977 1409.737
[9] 0.000 1424.277
> rowVars(tmp5,na.rm=TRUE)
[1] 7875.71059 94.21798 78.25636 36.29137 79.66910 66.37717
[7] 75.59537 105.41909 NA 54.51813
> rowSd(tmp5,na.rm=TRUE)
[1] 88.745200 9.706595 8.846262 6.024232 8.925755 8.147218 8.694560
[8] 10.267380 NA 7.383639
> rowMax(tmp5,na.rm=TRUE)
[1] 464.09153 90.81793 90.96510 82.39770 91.49576 87.30004 86.49421
[8] 88.12020 NA 83.76616
> rowMin(tmp5,na.rm=TRUE)
[1] 56.06291 53.75548 60.53412 61.28409 57.60986 55.08755 55.65290 56.52651
[9] NA 56.70492
>
>
> # now set an entire col to NA
>
>
> tmp5[,which.col] <- NA
> colMeans(tmp5,na.rm=TRUE)
[1] NaN 66.44186 71.29579 68.02584 72.59115 71.87454 66.93002 73.40678
[9] 69.07963 70.83568 73.67258 73.14253 74.18414 71.00781 71.75228 68.67247
[17] 75.60431 73.24867 72.92272 68.21032
> colSums(tmp5,na.rm=TRUE)
[1] 0.0000 597.9768 641.6621 612.2326 653.3203 646.8709 602.3702 660.6611
[9] 621.7167 637.5211 663.0532 658.2827 667.6573 639.0703 645.7705 618.0523
[17] 680.4388 659.2380 656.3045 613.8928
> colVars(tmp5,na.rm=TRUE)
[1] NA 39.47745 56.43320 30.44838 55.09217 55.07097 14.61734
[8] 138.62641 48.56442 109.25411 120.97592 60.94572 70.84545 59.61787
[15] 105.11359 72.52716 109.44315 92.39724 23.40325 117.35809
> colSd(tmp5,na.rm=TRUE)
[1] NA 6.283108 7.512203 5.518005 7.422410 7.420982 3.823263
[8] 11.773972 6.968818 10.452469 10.998906 7.806774 8.416974 7.721261
[15] 10.252492 8.516288 10.461508 9.612348 4.837690 10.833194
> colMax(tmp5,na.rm=TRUE)
[1] -Inf 74.94036 82.39770 77.40231 82.11319 90.81793 73.43942 85.51094
[9] 80.33588 88.93336 88.12020 78.48917 87.30004 83.61109 86.49421 83.30314
[17] 90.96510 91.49576 79.62450 83.76616
> colMin(tmp5,na.rm=TRUE)
[1] Inf 56.52651 61.27379 61.09096 59.94173 65.77545 62.35500 53.75548
[9] 61.73536 57.11269 55.08755 58.91640 62.66511 60.04278 59.82470 56.70492
[17] 62.38349 61.73116 63.45138 56.06291
>
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 3
> which.col <- 1
> cat(which.row," ",which.col,"\n")
3 1
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> rowVars(tmp5,na.rm=TRUE)
[1] 433.24207 140.00413 222.02059 125.96200 146.52873 321.51734 87.89325
[8] 170.90202 108.79786 181.68400
> apply(copymatrix,1,var,na.rm=TRUE)
[1] 433.24207 140.00413 222.02059 125.96200 146.52873 321.51734 87.89325
[8] 170.90202 108.79786 181.68400
>
>
>
> copymatrix <- matrix(rnorm(200,150,15),10,20)
>
> tmp5[1:10,1:20] <- copymatrix
> which.row <- 1
> which.col <- 3
> cat(which.row," ",which.col,"\n")
1 3
> tmp5[which.row,which.col] <- NA
> copymatrix[which.row,which.col] <- NA
>
> colVars(tmp5,na.rm=TRUE)-apply(copymatrix,2,var,na.rm=TRUE)
[1] 1.421085e-13 2.842171e-14 -1.136868e-13 -1.278977e-13 0.000000e+00
[6] -1.705303e-13 -1.136868e-13 1.421085e-14 -5.684342e-14 5.684342e-14
[11] 5.684342e-14 -1.136868e-13 -1.136868e-13 5.684342e-14 0.000000e+00
[16] -2.273737e-13 5.684342e-14 2.842171e-14 -2.842171e-13 -1.136868e-13
>
>
>
>
>
>
>
>
>
>
> ## making sure these things agree
> ##
> ## first when there is no NA
>
>
>
> agree.checks <- function(buff.matrix,r.matrix,err.tol=1e-10){
+
+ if (Max(buff.matrix,na.rm=TRUE) != max(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Max")
+ }
+
+
+ if (Min(buff.matrix,na.rm=TRUE) != min(r.matrix,na.rm=TRUE)){
+ stop("No agreement in Min")
+ }
+
+
+ if (abs(Sum(buff.matrix,na.rm=TRUE)- sum(r.matrix,na.rm=TRUE)) > err.tol){
+
+ cat(Sum(buff.matrix,na.rm=TRUE),"\n")
+ cat(sum(r.matrix,na.rm=TRUE),"\n")
+ cat(Sum(buff.matrix,na.rm=TRUE) - sum(r.matrix,na.rm=TRUE),"\n")
+
+ stop("No agreement in Sum")
+ }
+
+ if (abs(mean(buff.matrix,na.rm=TRUE) - mean(r.matrix,na.rm=TRUE)) > err.tol){
+ stop("No agreement in mean")
+ }
+
+
+ if(abs(Var(buff.matrix,na.rm=TRUE) - var(as.vector(r.matrix),na.rm=TRUE)) > err.tol){
+ stop("No agreement in Var")
+ }
+
+
+
+ if(any(abs(rowMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,mean,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowMeans")
+ }
+
+
+ if(any(abs(colMeans(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,mean,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colMeans")
+ }
+
+
+ if(any(abs(rowSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in rowSums")
+ }
+
+
+ if(any(abs(colSums(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,sum,na.rm=TRUE))> err.tol,na.rm=TRUE)){
+ stop("No agreement in colSums")
+ }
+
+ ### this is to get around the fact that R doesn't like to compute NA on an entire vector of NA when
+ ### computing variance
+ my.Var <- function(x,na.rm=FALSE){
+ if (all(is.na(x))){
+ return(NA)
+ } else {
+ var(x,na.rm=na.rm)
+ }
+
+ }
+
+ if(any(abs(rowVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(colVars(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,my.Var,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in rowVars")
+ }
+
+
+ if(any(abs(rowMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+ if(any(abs(colMax(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,max,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMax")
+ }
+
+
+
+ if(any(abs(rowMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,1,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+
+ if(any(abs(colMin(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,min,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMin")
+ }
+
+ if(any(abs(colMedians(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,median,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colMedian")
+ }
+
+ if(any(abs(colRanges(buff.matrix,na.rm=TRUE) - apply(r.matrix,2,range,na.rm=TRUE)) > err.tol,na.rm=TRUE)){
+ stop("No agreement in colRanges")
+ }
+
+
+
+ }
>
>
>
>
>
>
>
>
>
> for (rep in 1:20){
+ copymatrix <- matrix(rnorm(200,150,15),10,20)
+
+ tmp5[1:10,1:20] <- copymatrix
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ## now lets assign some NA values and check agreement
+
+ which.row <- sample(1:10,1,replace=TRUE)
+ which.col <- sample(1:20,1,replace=TRUE)
+
+ cat(which.row," ",which.col,"\n")
+
+ tmp5[which.row,which.col] <- NA
+ copymatrix[which.row,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ## make an entire row NA
+ tmp5[which.row,] <- NA
+ copymatrix[which.row,] <- NA
+
+
+ agree.checks(tmp5,copymatrix)
+
+ ### also make an entire col NA
+ tmp5[,which.col] <- NA
+ copymatrix[,which.col] <- NA
+
+ agree.checks(tmp5,copymatrix)
+
+ ### now make 1 element non NA with NA in the rest of row and column
+
+ tmp5[which.row,which.col] <- rnorm(1,150,15)
+ copymatrix[which.row,which.col] <- tmp5[which.row,which.col]
+
+ agree.checks(tmp5,copymatrix)
+ }
3 4
4 4
8 1
5 5
10 19
8 14
3 7
9 14
6 6
1 5
6 19
5 18
6 1
3 17
4 1
1 3
7 12
5 17
10 7
9 14
There were 50 or more warnings (use warnings() to see the first 50)
>
>
> ### now test 1 by n and n by 1 matrix
>
>
> err.tol <- 1e-12
>
> rm(tmp5)
>
> dataset1 <- rnorm(100)
> dataset2 <- rnorm(100)
>
> tmp <- createBufferedMatrix(1,100)
> tmp[1,] <- dataset1
>
> tmp2 <- createBufferedMatrix(100,1)
> tmp2[,1] <- dataset2
>
>
>
>
>
> Max(tmp)
[1] 1.764075
> Min(tmp)
[1] -1.938143
> mean(tmp)
[1] -0.01979604
> Sum(tmp)
[1] -1.979604
> Var(tmp)
[1] 0.794736
>
> rowMeans(tmp)
[1] -0.01979604
> rowSums(tmp)
[1] -1.979604
> rowVars(tmp)
[1] 0.794736
> rowSd(tmp)
[1] 0.8914797
> rowMax(tmp)
[1] 1.764075
> rowMin(tmp)
[1] -1.938143
>
> colMeans(tmp)
[1] 0.63274850 0.78235330 -1.39110494 1.49899076 0.44107394 -0.81738890
[7] -1.03945831 -1.93814303 -0.59619868 0.19650997 1.41081040 1.19634858
[13] -0.53429213 -0.96577833 -0.16483652 0.31542813 0.95054533 0.69311989
[19] -1.40358248 0.73128504 -0.49427624 -0.09573619 1.33572533 1.23508863
[25] -1.37247113 0.70954297 -0.75672880 0.31841357 -1.39676708 -1.75540150
[31] 1.26823817 0.49342338 0.68502404 0.41281770 -0.33228226 -0.67731242
[37] 0.83184916 0.89569914 0.14364255 0.13094382 0.21312081 0.08012731
[43] -0.28238351 0.07830084 -0.57243772 0.59634393 -0.73857959 -0.90891809
[49] -1.32449997 0.87534839 1.26066862 -0.04730559 0.30087255 -1.20310829
[55] -1.20635958 -0.45927365 0.16210814 1.76407451 0.54457673 -1.51591143
[61] 0.31983174 -0.43326290 0.03960714 -1.18061358 -0.05200660 1.12838302
[67] -1.32332187 1.34507016 -0.24076895 -1.45964853 0.82461043 0.39327851
[73] 0.48284805 0.11774545 1.10347071 -0.28790063 -0.75959406 0.55208718
[79] 0.43824169 -1.41826445 -0.40905745 -0.54613167 0.57674370 0.10504222
[85] -0.62325893 -1.10944949 -0.11140188 1.17726843 -0.90773768 -0.59587076
[91] 0.04726533 -0.36407513 1.74584858 1.34483994 -0.20429239 0.83160011
[97] -0.69393679 -0.45595381 0.58668863 -1.15815536
> colSums(tmp)
[1] 0.63274850 0.78235330 -1.39110494 1.49899076 0.44107394 -0.81738890
[7] -1.03945831 -1.93814303 -0.59619868 0.19650997 1.41081040 1.19634858
[13] -0.53429213 -0.96577833 -0.16483652 0.31542813 0.95054533 0.69311989
[19] -1.40358248 0.73128504 -0.49427624 -0.09573619 1.33572533 1.23508863
[25] -1.37247113 0.70954297 -0.75672880 0.31841357 -1.39676708 -1.75540150
[31] 1.26823817 0.49342338 0.68502404 0.41281770 -0.33228226 -0.67731242
[37] 0.83184916 0.89569914 0.14364255 0.13094382 0.21312081 0.08012731
[43] -0.28238351 0.07830084 -0.57243772 0.59634393 -0.73857959 -0.90891809
[49] -1.32449997 0.87534839 1.26066862 -0.04730559 0.30087255 -1.20310829
[55] -1.20635958 -0.45927365 0.16210814 1.76407451 0.54457673 -1.51591143
[61] 0.31983174 -0.43326290 0.03960714 -1.18061358 -0.05200660 1.12838302
[67] -1.32332187 1.34507016 -0.24076895 -1.45964853 0.82461043 0.39327851
[73] 0.48284805 0.11774545 1.10347071 -0.28790063 -0.75959406 0.55208718
[79] 0.43824169 -1.41826445 -0.40905745 -0.54613167 0.57674370 0.10504222
[85] -0.62325893 -1.10944949 -0.11140188 1.17726843 -0.90773768 -0.59587076
[91] 0.04726533 -0.36407513 1.74584858 1.34483994 -0.20429239 0.83160011
[97] -0.69393679 -0.45595381 0.58668863 -1.15815536
> colVars(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colSd(tmp)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> colMax(tmp)
[1] 0.63274850 0.78235330 -1.39110494 1.49899076 0.44107394 -0.81738890
[7] -1.03945831 -1.93814303 -0.59619868 0.19650997 1.41081040 1.19634858
[13] -0.53429213 -0.96577833 -0.16483652 0.31542813 0.95054533 0.69311989
[19] -1.40358248 0.73128504 -0.49427624 -0.09573619 1.33572533 1.23508863
[25] -1.37247113 0.70954297 -0.75672880 0.31841357 -1.39676708 -1.75540150
[31] 1.26823817 0.49342338 0.68502404 0.41281770 -0.33228226 -0.67731242
[37] 0.83184916 0.89569914 0.14364255 0.13094382 0.21312081 0.08012731
[43] -0.28238351 0.07830084 -0.57243772 0.59634393 -0.73857959 -0.90891809
[49] -1.32449997 0.87534839 1.26066862 -0.04730559 0.30087255 -1.20310829
[55] -1.20635958 -0.45927365 0.16210814 1.76407451 0.54457673 -1.51591143
[61] 0.31983174 -0.43326290 0.03960714 -1.18061358 -0.05200660 1.12838302
[67] -1.32332187 1.34507016 -0.24076895 -1.45964853 0.82461043 0.39327851
[73] 0.48284805 0.11774545 1.10347071 -0.28790063 -0.75959406 0.55208718
[79] 0.43824169 -1.41826445 -0.40905745 -0.54613167 0.57674370 0.10504222
[85] -0.62325893 -1.10944949 -0.11140188 1.17726843 -0.90773768 -0.59587076
[91] 0.04726533 -0.36407513 1.74584858 1.34483994 -0.20429239 0.83160011
[97] -0.69393679 -0.45595381 0.58668863 -1.15815536
> colMin(tmp)
[1] 0.63274850 0.78235330 -1.39110494 1.49899076 0.44107394 -0.81738890
[7] -1.03945831 -1.93814303 -0.59619868 0.19650997 1.41081040 1.19634858
[13] -0.53429213 -0.96577833 -0.16483652 0.31542813 0.95054533 0.69311989
[19] -1.40358248 0.73128504 -0.49427624 -0.09573619 1.33572533 1.23508863
[25] -1.37247113 0.70954297 -0.75672880 0.31841357 -1.39676708 -1.75540150
[31] 1.26823817 0.49342338 0.68502404 0.41281770 -0.33228226 -0.67731242
[37] 0.83184916 0.89569914 0.14364255 0.13094382 0.21312081 0.08012731
[43] -0.28238351 0.07830084 -0.57243772 0.59634393 -0.73857959 -0.90891809
[49] -1.32449997 0.87534839 1.26066862 -0.04730559 0.30087255 -1.20310829
[55] -1.20635958 -0.45927365 0.16210814 1.76407451 0.54457673 -1.51591143
[61] 0.31983174 -0.43326290 0.03960714 -1.18061358 -0.05200660 1.12838302
[67] -1.32332187 1.34507016 -0.24076895 -1.45964853 0.82461043 0.39327851
[73] 0.48284805 0.11774545 1.10347071 -0.28790063 -0.75959406 0.55208718
[79] 0.43824169 -1.41826445 -0.40905745 -0.54613167 0.57674370 0.10504222
[85] -0.62325893 -1.10944949 -0.11140188 1.17726843 -0.90773768 -0.59587076
[91] 0.04726533 -0.36407513 1.74584858 1.34483994 -0.20429239 0.83160011
[97] -0.69393679 -0.45595381 0.58668863 -1.15815536
> colMedians(tmp)
[1] 0.63274850 0.78235330 -1.39110494 1.49899076 0.44107394 -0.81738890
[7] -1.03945831 -1.93814303 -0.59619868 0.19650997 1.41081040 1.19634858
[13] -0.53429213 -0.96577833 -0.16483652 0.31542813 0.95054533 0.69311989
[19] -1.40358248 0.73128504 -0.49427624 -0.09573619 1.33572533 1.23508863
[25] -1.37247113 0.70954297 -0.75672880 0.31841357 -1.39676708 -1.75540150
[31] 1.26823817 0.49342338 0.68502404 0.41281770 -0.33228226 -0.67731242
[37] 0.83184916 0.89569914 0.14364255 0.13094382 0.21312081 0.08012731
[43] -0.28238351 0.07830084 -0.57243772 0.59634393 -0.73857959 -0.90891809
[49] -1.32449997 0.87534839 1.26066862 -0.04730559 0.30087255 -1.20310829
[55] -1.20635958 -0.45927365 0.16210814 1.76407451 0.54457673 -1.51591143
[61] 0.31983174 -0.43326290 0.03960714 -1.18061358 -0.05200660 1.12838302
[67] -1.32332187 1.34507016 -0.24076895 -1.45964853 0.82461043 0.39327851
[73] 0.48284805 0.11774545 1.10347071 -0.28790063 -0.75959406 0.55208718
[79] 0.43824169 -1.41826445 -0.40905745 -0.54613167 0.57674370 0.10504222
[85] -0.62325893 -1.10944949 -0.11140188 1.17726843 -0.90773768 -0.59587076
[91] 0.04726533 -0.36407513 1.74584858 1.34483994 -0.20429239 0.83160011
[97] -0.69393679 -0.45595381 0.58668863 -1.15815536
> colRanges(tmp)
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
[1,] 0.6327485 0.7823533 -1.391105 1.498991 0.4410739 -0.8173889 -1.039458
[2,] 0.6327485 0.7823533 -1.391105 1.498991 0.4410739 -0.8173889 -1.039458
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
[1,] -1.938143 -0.5961987 0.19651 1.41081 1.196349 -0.5342921 -0.9657783
[2,] -1.938143 -0.5961987 0.19651 1.41081 1.196349 -0.5342921 -0.9657783
[,15] [,16] [,17] [,18] [,19] [,20] [,21]
[1,] -0.1648365 0.3154281 0.9505453 0.6931199 -1.403582 0.731285 -0.4942762
[2,] -0.1648365 0.3154281 0.9505453 0.6931199 -1.403582 0.731285 -0.4942762
[,22] [,23] [,24] [,25] [,26] [,27] [,28]
[1,] -0.09573619 1.335725 1.235089 -1.372471 0.709543 -0.7567288 0.3184136
[2,] -0.09573619 1.335725 1.235089 -1.372471 0.709543 -0.7567288 0.3184136
[,29] [,30] [,31] [,32] [,33] [,34] [,35]
[1,] -1.396767 -1.755401 1.268238 0.4934234 0.685024 0.4128177 -0.3322823
[2,] -1.396767 -1.755401 1.268238 0.4934234 0.685024 0.4128177 -0.3322823
[,36] [,37] [,38] [,39] [,40] [,41] [,42]
[1,] -0.6773124 0.8318492 0.8956991 0.1436425 0.1309438 0.2131208 0.08012731
[2,] -0.6773124 0.8318492 0.8956991 0.1436425 0.1309438 0.2131208 0.08012731
[,43] [,44] [,45] [,46] [,47] [,48] [,49]
[1,] -0.2823835 0.07830084 -0.5724377 0.5963439 -0.7385796 -0.9089181 -1.3245
[2,] -0.2823835 0.07830084 -0.5724377 0.5963439 -0.7385796 -0.9089181 -1.3245
[,50] [,51] [,52] [,53] [,54] [,55] [,56]
[1,] 0.8753484 1.260669 -0.04730559 0.3008725 -1.203108 -1.20636 -0.4592737
[2,] 0.8753484 1.260669 -0.04730559 0.3008725 -1.203108 -1.20636 -0.4592737
[,57] [,58] [,59] [,60] [,61] [,62] [,63]
[1,] 0.1621081 1.764075 0.5445767 -1.515911 0.3198317 -0.4332629 0.03960714
[2,] 0.1621081 1.764075 0.5445767 -1.515911 0.3198317 -0.4332629 0.03960714
[,64] [,65] [,66] [,67] [,68] [,69] [,70]
[1,] -1.180614 -0.0520066 1.128383 -1.323322 1.34507 -0.2407689 -1.459649
[2,] -1.180614 -0.0520066 1.128383 -1.323322 1.34507 -0.2407689 -1.459649
[,71] [,72] [,73] [,74] [,75] [,76] [,77]
[1,] 0.8246104 0.3932785 0.482848 0.1177455 1.103471 -0.2879006 -0.7595941
[2,] 0.8246104 0.3932785 0.482848 0.1177455 1.103471 -0.2879006 -0.7595941
[,78] [,79] [,80] [,81] [,82] [,83] [,84]
[1,] 0.5520872 0.4382417 -1.418264 -0.4090574 -0.5461317 0.5767437 0.1050422
[2,] 0.5520872 0.4382417 -1.418264 -0.4090574 -0.5461317 0.5767437 0.1050422
[,85] [,86] [,87] [,88] [,89] [,90] [,91]
[1,] -0.6232589 -1.109449 -0.1114019 1.177268 -0.9077377 -0.5958708 0.04726533
[2,] -0.6232589 -1.109449 -0.1114019 1.177268 -0.9077377 -0.5958708 0.04726533
[,92] [,93] [,94] [,95] [,96] [,97] [,98]
[1,] -0.3640751 1.745849 1.34484 -0.2042924 0.8316001 -0.6939368 -0.4559538
[2,] -0.3640751 1.745849 1.34484 -0.2042924 0.8316001 -0.6939368 -0.4559538
[,99] [,100]
[1,] 0.5866886 -1.158155
[2,] 0.5866886 -1.158155
>
>
> Max(tmp2)
[1] 3.155901
> Min(tmp2)
[1] -2.436868
> mean(tmp2)
[1] 0.0008964379
> Sum(tmp2)
[1] 0.08964379
> Var(tmp2)
[1] 0.9166761
>
> rowMeans(tmp2)
[1] 1.078969270 1.024172370 0.916631281 -1.072321109 -1.174542630
[6] -0.860233257 1.509981179 -0.802045304 1.479163385 -0.291353202
[11] 0.017511968 0.417997654 -0.783149834 -0.640411749 0.612656218
[16] 0.121643058 1.585361747 -0.061371715 0.051437669 -1.451846907
[21] -0.404562652 0.753617437 0.154514211 -2.436867557 -0.063316081
[26] -0.372938395 0.237260216 0.311333764 0.426822266 -0.339366110
[31] -0.165720049 1.279335459 -1.165751469 1.764145393 0.271937651
[36] -1.549710132 -0.808223076 -0.821370278 -0.410388455 1.636164591
[41] -1.170722011 -1.285554583 -0.872285611 -0.316729208 -0.966382390
[46] -0.135068111 -0.625126863 0.727694918 -1.418927271 0.012737714
[51] -0.147939513 -0.338589397 -0.955146681 0.276337237 -1.471092563
[56] 0.191400209 -0.249699743 -1.158121090 0.921125631 0.206192629
[61] -1.620075628 -0.419192592 0.200752549 1.954992416 3.155900730
[66] 0.206507617 0.465332100 -1.141673455 0.035007001 -1.059044463
[71] -1.506414854 -0.478946332 0.059450828 0.232193708 0.622939247
[76] 0.909533767 -1.096843292 0.206797493 -0.739160009 0.417201631
[81] 0.484013834 0.006716657 0.783361189 0.252018866 -0.330347299
[86] -0.140718245 0.167100287 -0.704148888 0.475005754 0.682127733
[91] 0.374888673 0.285517039 -0.014089608 1.364641250 0.671338614
[96] 0.700287194 1.081633572 -0.303570855 2.817236816 -0.167897381
> rowSums(tmp2)
[1] 1.078969270 1.024172370 0.916631281 -1.072321109 -1.174542630
[6] -0.860233257 1.509981179 -0.802045304 1.479163385 -0.291353202
[11] 0.017511968 0.417997654 -0.783149834 -0.640411749 0.612656218
[16] 0.121643058 1.585361747 -0.061371715 0.051437669 -1.451846907
[21] -0.404562652 0.753617437 0.154514211 -2.436867557 -0.063316081
[26] -0.372938395 0.237260216 0.311333764 0.426822266 -0.339366110
[31] -0.165720049 1.279335459 -1.165751469 1.764145393 0.271937651
[36] -1.549710132 -0.808223076 -0.821370278 -0.410388455 1.636164591
[41] -1.170722011 -1.285554583 -0.872285611 -0.316729208 -0.966382390
[46] -0.135068111 -0.625126863 0.727694918 -1.418927271 0.012737714
[51] -0.147939513 -0.338589397 -0.955146681 0.276337237 -1.471092563
[56] 0.191400209 -0.249699743 -1.158121090 0.921125631 0.206192629
[61] -1.620075628 -0.419192592 0.200752549 1.954992416 3.155900730
[66] 0.206507617 0.465332100 -1.141673455 0.035007001 -1.059044463
[71] -1.506414854 -0.478946332 0.059450828 0.232193708 0.622939247
[76] 0.909533767 -1.096843292 0.206797493 -0.739160009 0.417201631
[81] 0.484013834 0.006716657 0.783361189 0.252018866 -0.330347299
[86] -0.140718245 0.167100287 -0.704148888 0.475005754 0.682127733
[91] 0.374888673 0.285517039 -0.014089608 1.364641250 0.671338614
[96] 0.700287194 1.081633572 -0.303570855 2.817236816 -0.167897381
> rowVars(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowSd(tmp2)
[1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[51] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
[76] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> rowMax(tmp2)
[1] 1.078969270 1.024172370 0.916631281 -1.072321109 -1.174542630
[6] -0.860233257 1.509981179 -0.802045304 1.479163385 -0.291353202
[11] 0.017511968 0.417997654 -0.783149834 -0.640411749 0.612656218
[16] 0.121643058 1.585361747 -0.061371715 0.051437669 -1.451846907
[21] -0.404562652 0.753617437 0.154514211 -2.436867557 -0.063316081
[26] -0.372938395 0.237260216 0.311333764 0.426822266 -0.339366110
[31] -0.165720049 1.279335459 -1.165751469 1.764145393 0.271937651
[36] -1.549710132 -0.808223076 -0.821370278 -0.410388455 1.636164591
[41] -1.170722011 -1.285554583 -0.872285611 -0.316729208 -0.966382390
[46] -0.135068111 -0.625126863 0.727694918 -1.418927271 0.012737714
[51] -0.147939513 -0.338589397 -0.955146681 0.276337237 -1.471092563
[56] 0.191400209 -0.249699743 -1.158121090 0.921125631 0.206192629
[61] -1.620075628 -0.419192592 0.200752549 1.954992416 3.155900730
[66] 0.206507617 0.465332100 -1.141673455 0.035007001 -1.059044463
[71] -1.506414854 -0.478946332 0.059450828 0.232193708 0.622939247
[76] 0.909533767 -1.096843292 0.206797493 -0.739160009 0.417201631
[81] 0.484013834 0.006716657 0.783361189 0.252018866 -0.330347299
[86] -0.140718245 0.167100287 -0.704148888 0.475005754 0.682127733
[91] 0.374888673 0.285517039 -0.014089608 1.364641250 0.671338614
[96] 0.700287194 1.081633572 -0.303570855 2.817236816 -0.167897381
> rowMin(tmp2)
[1] 1.078969270 1.024172370 0.916631281 -1.072321109 -1.174542630
[6] -0.860233257 1.509981179 -0.802045304 1.479163385 -0.291353202
[11] 0.017511968 0.417997654 -0.783149834 -0.640411749 0.612656218
[16] 0.121643058 1.585361747 -0.061371715 0.051437669 -1.451846907
[21] -0.404562652 0.753617437 0.154514211 -2.436867557 -0.063316081
[26] -0.372938395 0.237260216 0.311333764 0.426822266 -0.339366110
[31] -0.165720049 1.279335459 -1.165751469 1.764145393 0.271937651
[36] -1.549710132 -0.808223076 -0.821370278 -0.410388455 1.636164591
[41] -1.170722011 -1.285554583 -0.872285611 -0.316729208 -0.966382390
[46] -0.135068111 -0.625126863 0.727694918 -1.418927271 0.012737714
[51] -0.147939513 -0.338589397 -0.955146681 0.276337237 -1.471092563
[56] 0.191400209 -0.249699743 -1.158121090 0.921125631 0.206192629
[61] -1.620075628 -0.419192592 0.200752549 1.954992416 3.155900730
[66] 0.206507617 0.465332100 -1.141673455 0.035007001 -1.059044463
[71] -1.506414854 -0.478946332 0.059450828 0.232193708 0.622939247
[76] 0.909533767 -1.096843292 0.206797493 -0.739160009 0.417201631
[81] 0.484013834 0.006716657 0.783361189 0.252018866 -0.330347299
[86] -0.140718245 0.167100287 -0.704148888 0.475005754 0.682127733
[91] 0.374888673 0.285517039 -0.014089608 1.364641250 0.671338614
[96] 0.700287194 1.081633572 -0.303570855 2.817236816 -0.167897381
>
> colMeans(tmp2)
[1] 0.0008964379
> colSums(tmp2)
[1] 0.08964379
> colVars(tmp2)
[1] 0.9166761
> colSd(tmp2)
[1] 0.9574321
> colMax(tmp2)
[1] 3.155901
> colMin(tmp2)
[1] -2.436868
> colMedians(tmp2)
[1] 0.01512484
> colRanges(tmp2)
[,1]
[1,] -2.436868
[2,] 3.155901
>
> dataset1 <- matrix(dataset1,1,100)
>
> agree.checks(tmp,dataset1)
>
> dataset2 <- matrix(dataset2,100,1)
> agree.checks(tmp2,dataset2)
>
>
> tmp <- createBufferedMatrix(10,10)
>
> tmp[1:10,1:10] <- rnorm(100)
> colApply(tmp,sum)
[1] -0.47709549 -5.80477312 -2.37816008 8.60913685 -4.60859341 0.06759068
[7] -1.29941004 -4.96434610 1.31432339 1.68887155
> colApply(tmp,quantile)[,1]
[,1]
[1,] -0.5569632
[2,] -0.3714357
[3,] -0.2528812
[4,] 0.3759180
[5,] 0.5927817
>
> rowApply(tmp,sum)
[1] 3.7541431 2.2501152 -4.2402714 -1.8424903 -6.9640531 -2.6330094
[7] 3.1060680 -0.7633501 0.5414019 -1.0610097
> rowApply(tmp,rank)[1:10,]
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10]
[1,] 5 4 9 4 6 4 3 8 6 5
[2,] 1 8 4 3 4 5 1 6 1 3
[3,] 8 7 5 7 2 2 7 3 3 1
[4,] 6 10 8 8 7 10 10 10 8 9
[5,] 2 1 2 6 9 7 2 4 4 8
[6,] 4 9 6 5 10 3 9 1 10 2
[7,] 3 3 1 10 8 8 6 5 2 10
[8,] 9 6 3 2 1 1 5 2 5 4
[9,] 7 2 7 9 5 9 4 7 7 7
[10,] 10 5 10 1 3 6 8 9 9 6
>
> tmp <- createBufferedMatrix(5,20)
>
> tmp[1:5,1:20] <- rnorm(100)
> colApply(tmp,sum)
[1] -3.8006381 -3.1156538 2.1375625 3.4220125 -0.3051558 2.3010519
[7] 4.9611267 -1.4161897 -1.3920122 2.8773232 0.7348776 1.8348509
[13] -1.6354401 -0.7926676 -3.9455759 3.7718460 -3.6940557 1.4099657
[19] 1.5845939 -2.1557692
> colApply(tmp,quantile)[,1]
[,1]
[1,] -1.1867829
[2,] -0.8565729
[3,] -0.7104209
[4,] -0.6695515
[5,] -0.3773100
>
> rowApply(tmp,sum)
[1] -2.1302840 2.9791095 -0.5162424 6.5486216 -4.0991519
> rowApply(tmp,rank)[1:5,]
[,1] [,2] [,3] [,4] [,5]
[1,] 3 4 6 3 7
[2,] 8 15 3 5 1
[3,] 9 18 13 12 15
[4,] 13 16 12 19 17
[5,] 1 11 4 20 14
>
>
> as.matrix(tmp)
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] -1.1867829 -0.61575099 -0.3819414 0.4530520 -1.5549613 0.36620604
[2,] -0.8565729 0.89439582 1.0367609 0.8947493 0.3603644 0.88854172
[3,] -0.7104209 -1.20171981 0.2860665 0.2494595 -1.1146468 1.20369227
[4,] -0.6695515 -0.06882626 0.6873510 1.2295464 1.4988125 0.09208136
[5,] -0.3773100 -2.12375258 0.5093254 0.5952053 0.5052753 -0.24946946
[,7] [,8] [,9] [,10] [,11] [,12]
[1,] 0.4747803 -0.8008532 1.1755544 0.7089931 0.003396685 0.455729114
[2,] 1.5749839 -0.2986415 -1.3920667 0.4194690 0.084330808 0.525619806
[3,] 1.4746115 -0.1347670 -0.4538101 0.9738610 1.622090262 0.001523227
[4,] 0.4560634 -0.7266297 0.4385332 0.4240895 -2.338800937 0.905409426
[5,] 0.9806876 0.5447018 -1.1602230 0.3509107 1.363860773 -0.053430672
[,13] [,14] [,15] [,16] [,17] [,18]
[1,] 0.5629003 0.08818773 -1.1720043 1.32294600 -1.3008107 1.0357956
[2,] 0.9445846 -1.47686769 -0.4670648 2.38776122 -0.8527891 0.1440925
[3,] -1.9001900 -0.53666618 -2.4183793 -0.16159160 -0.7608778 1.0945986
[4,] 0.6943694 0.10739500 -0.2237203 0.16134511 0.9319895 1.0629255
[5,] -1.9371045 1.02528350 0.3355928 0.06138524 -1.7115675 -1.9274465
[,19] [,20]
[1,] -0.6347341 -1.1299865
[2,] -0.1202610 -1.7122808
[3,] 0.8495077 1.1214163
[4,] 1.0956687 0.7905704
[5,] 0.3944126 -1.2254887
>
>
> is.BufferedMatrix(tmp)
[1] TRUE
>
> as.BufferedMatrix(as.matrix(tmp))
BufferedMatrix object
Matrix size: 5 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 800 bytes.
>
>
>
> subBufferedMatrix(tmp,1:5,1:5)
BufferedMatrix object
Matrix size: 5 5
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 648 bytes.
Disk usage : 200 bytes.
> subBufferedMatrix(tmp,,5:8)
BufferedMatrix object
Matrix size: 5 4
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 559 bytes.
Disk usage : 160 bytes.
> subBufferedMatrix(tmp,1:3,)
BufferedMatrix object
Matrix size: 3 20
Buffer size: 1 1
Directory: /home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests
Prefix: BM
Mode: Col mode
Read Only: FALSE
Memory usage : 1.9 Kilobytes.
Disk usage : 480 bytes.
>
>
> rm(tmp)
>
>
> ###
> ### Testing colnames and rownames
> ###
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
>
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7
row1 -0.6798317 0.7378112 -2.467304 0.4969277 -0.402309 2.155684 -1.652942
col8 col9 col10 col11 col12 col13 col14
row1 1.144718 -2.564575 0.6390779 1.541609 0.4878025 0.2353455 0.06179008
col15 col16 col17 col18 col19 col20
row1 1.862484 -1.933635 -0.4028223 -0.6665062 0.4656399 -0.3678849
> tmp[,"col10"]
col10
row1 0.6390779
row2 1.7635125
row3 -1.8124033
row4 1.1744353
row5 -0.2872774
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7
row1 -0.6798317 0.7378112 -2.4673041 0.4969277 -0.4023090 2.1556843 -1.6529420
row5 3.1473883 0.7488615 0.3638003 0.5623590 -0.4056956 -0.5448667 -0.4940343
col8 col9 col10 col11 col12 col13 col14
row1 1.1447181 -2.5645750 0.6390779 1.541609 0.4878025 0.2353455 0.06179008
row5 0.4461133 0.1847636 -0.2872774 2.015750 0.7545827 0.5863286 0.61950882
col15 col16 col17 col18 col19 col20
row1 1.862484 -1.933635 -0.4028223 -0.6665062 0.46563987 -0.3678849
row5 0.113131 1.440835 0.5563735 0.9825117 0.09903923 0.6582724
> tmp[,c("col6","col20")]
col6 col20
row1 2.1556843 -0.36788486
row2 0.7946526 0.84180806
row3 0.1919684 -0.02693014
row4 0.3764184 0.55524964
row5 -0.5448667 0.65827243
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 2.1556843 -0.3678849
row5 -0.5448667 0.6582724
>
>
>
>
> tmp["row1",] <- rnorm(20,mean=10)
> tmp[,"col10"] <- rnorm(5,mean=30)
> tmp[c("row1","row5"),] <- rnorm(40,mean=50)
> tmp[,c("col6","col20")] <- rnorm(10,mean=75)
> tmp[c("row1","row5"),c("col6","col20")] <- rnorm(4,mean=105)
>
> tmp["row1",]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.80941 49.73149 49.66505 50.54481 51.76572 105.5605 49.60851 49.56442
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.64374 49.20121 51.37657 49.97456 51.13172 46.9322 48.81661 50.26219
col17 col18 col19 col20
row1 49.39725 47.9402 48.34741 103.6764
> tmp[,"col10"]
col10
row1 49.20121
row2 32.41489
row3 30.82969
row4 29.97279
row5 51.04704
> tmp[c("row1","row5"),]
col1 col2 col3 col4 col5 col6 col7 col8
row1 49.80941 49.73149 49.66505 50.54481 51.76572 105.5605 49.60851 49.56442
row5 51.20789 49.68793 49.31758 49.59088 49.97494 105.4823 49.95532 50.53932
col9 col10 col11 col12 col13 col14 col15 col16
row1 49.64374 49.20121 51.37657 49.97456 51.13172 46.93220 48.81661 50.26219
row5 51.09365 51.04704 47.95915 48.96950 50.25644 50.11659 50.28077 51.79550
col17 col18 col19 col20
row1 49.39725 47.9402 48.34741 103.6764
row5 49.12424 50.8165 49.13268 104.8310
> tmp[,c("col6","col20")]
col6 col20
row1 105.56051 103.67636
row2 73.55167 75.43622
row3 73.34370 73.22461
row4 74.38090 75.04920
row5 105.48230 104.83099
> tmp[c("row1","row5"),c("col6","col20")]
col6 col20
row1 105.5605 103.6764
row5 105.4823 104.8310
>
>
> subBufferedMatrix(tmp,c("row1","row5"),c("col6","col20"))[1:2,1:2]
col6 col20
row1 105.5605 103.6764
row5 105.4823 104.8310
>
>
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
>
> tmp[,"col13"]
col13
[1,] -0.5890813
[2,] 0.2344832
[3,] -0.8049236
[4,] 1.7110926
[5,] -0.1200574
> tmp[,c("col17","col7")]
col17 col7
[1,] 1.5474859 1.16881842
[2,] -1.5716895 0.65646174
[3,] -0.4996638 1.64717800
[4,] -0.6004760 0.91519079
[5,] -0.3705608 -0.07074425
>
> subBufferedMatrix(tmp,,c("col6","col20"))[,1:2]
col6 col20
[1,] 1.74950242 -0.69447289
[2,] 0.04324524 -0.09873394
[3,] -0.47863052 1.28764743
[4,] 0.34075108 1.05462568
[5,] -1.31419513 -1.41773851
> subBufferedMatrix(tmp,1,c("col6"))[,1]
col1
[1,] 1.749502
> subBufferedMatrix(tmp,1:2,c("col6"))[,1]
col6
[1,] 1.74950242
[2,] 0.04324524
>
>
>
> tmp <- createBufferedMatrix(5,20)
> tmp[1:5,1:20] <- rnorm(100)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
>
>
>
> subBufferedMatrix(tmp,c("row3","row1"),)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row3 -0.9449842745 -0.2995303 -0.31642175 0.1797161 0.184861 0.9962404 3.133284
row1 0.0006616044 0.1327245 -0.01379417 0.2540239 1.730395 0.2939690 1.166923
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row3 0.3830815 -0.7257851 0.1002805 -1.684042 0.9430979 1.402441 0.4092999
row1 0.9299910 0.1618153 -0.3419574 1.302514 -0.6009165 -1.184326 2.9608308
[,15] [,16] [,17] [,18] [,19] [,20]
row3 0.0719587 -1.585231 1.1399083 -0.4269127 1.4010948 0.06354949
row1 0.5138512 -1.229380 0.2721563 0.2253244 -0.4740252 1.27473492
> subBufferedMatrix(tmp,c("row2"),1:10)[,1:10]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row2 1.843411 1.460503 -1.636092 0.1052209 0.4157919 1.378133 0.2922931
[,8] [,9] [,10]
row2 -2.005656 -0.8410026 1.786399
> subBufferedMatrix(tmp,c("row5"),1:20)[,1:20]
[,1] [,2] [,3] [,4] [,5] [,6] [,7]
row5 1.835598 0.2023996 0.5435394 -0.4065458 0.3122503 -0.6804478 -0.3991666
[,8] [,9] [,10] [,11] [,12] [,13] [,14]
row5 -0.6091442 -0.006163035 0.9952835 0.5647492 1.472934 -1.160567 2.329168
[,15] [,16] [,17] [,18] [,19] [,20]
row5 0.4755681 -0.176416 1.460012 0.2690806 -0.2943364 -0.1912999
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> colnames(tmp)
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
> rownames(tmp)
[1] "row1" "row2" "row3" "row4" "row5"
>
>
> colnames(tmp) <- NULL
> rownames(tmp) <- NULL
>
> colnames(tmp)
NULL
> rownames(tmp)
NULL
>
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
>
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
> dimnames(tmp) <- NULL
>
> colnames(tmp) <- colnames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
> dimnames(tmp) <- NULL
> rownames(tmp) <- rownames(tmp,do.NULL=FALSE)
> dimnames(tmp)
[[1]]
[1] "row1" "row2" "row3" "row4" "row5"
[[2]]
NULL
>
> dimnames(tmp) <- list(NULL,c(colnames(tmp,do.NULL=FALSE)))
> dimnames(tmp)
[[1]]
NULL
[[2]]
[1] "col1" "col2" "col3" "col4" "col5" "col6" "col7" "col8" "col9"
[10] "col10" "col11" "col12" "col13" "col14" "col15" "col16" "col17" "col18"
[19] "col19" "col20"
>
>
>
> ###
> ### Testing logical indexing
> ###
> ###
>
> tmp <- createBufferedMatrix(230,15)
> tmp[1:230,1:15] <- rnorm(230*15)
> x <-tmp[1:230,1:15]
>
> for (rep in 1:10){
+ which.cols <- sample(c(TRUE,FALSE),15,replace=T)
+ which.rows <- sample(c(TRUE,FALSE),230,replace=T)
+
+ if (!all(tmp[which.rows,which.cols] == x[which.rows,which.cols])){
+ stop("No agreement when logical indexing\n")
+ }
+
+ if (!all(subBufferedMatrix(tmp,,which.cols)[,1:sum(which.cols)] == x[,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix cols\n")
+ }
+ if (!all(subBufferedMatrix(tmp,which.rows,)[1:sum(which.rows),] == x[which.rows,])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows\n")
+ }
+
+
+ if (!all(subBufferedMatrix(tmp,which.rows,which.cols)[1:sum(which.rows),1:sum(which.cols)]== x[which.rows,which.cols])){
+ stop("No agreement when logical indexing in subBufferedMatrix rows and columns\n")
+ }
+ }
>
>
> ##
> ## Test the ReadOnlyMode
> ##
>
> ReadOnlyMode(tmp)
<pointer: 0x58f126ec6f20>
> is.ReadOnlyMode(tmp)
[1] TRUE
>
> filenames(tmp)
[1] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b663f0ad8c"
[2] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b6f841321"
[3] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b65d45558a"
[4] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b65e3821c7"
[5] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b674c12020"
[6] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b67167b2d6"
[7] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b644214097"
[8] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b67cfd3559"
[9] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b65821d2c5"
[10] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b61de8d8bc"
[11] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b66bfc9fe0"
[12] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b623ac25de"
[13] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b626812dd0"
[14] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b6221a402c"
[15] "/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests/BM989b6475158d7"
>
>
> ### testing coercion functions
> ###
>
> tmp <- as(tmp,"matrix")
> tmp <- as(tmp,"BufferedMatrix")
>
>
>
> ### testing whether can move storage from one location to another
>
> MoveStorageDirectory(tmp,"NewDirectory",full.path=FALSE)
<pointer: 0x58f12626c590>
> MoveStorageDirectory(tmp,getwd(),full.path=TRUE)
<pointer: 0x58f12626c590>
Warning message:
In dir.create(new.directory) :
'/home/biocbuild/bbs-3.22-bioc/meat/BufferedMatrix.Rcheck/tests' already exists
>
>
> RowMode(tmp)
<pointer: 0x58f12626c590>
> rowMedians(tmp)
[1] -0.3609099112 -0.0337439595 0.2978222856 0.1170558539 -0.3693137129
[6] -0.2565673738 -1.0069113610 -0.7058289380 0.2849150678 0.2124687167
[11] -0.2265406026 0.4875231638 -0.0792004454 0.5164708891 0.0199515663
[16] 0.4643912667 0.3326482051 0.4077136797 0.0324930507 -0.1465045800
[21] -0.4551985396 0.5258146583 -0.1270171276 0.0532918410 0.7459178456
[26] -0.3114071920 -0.4049999344 -0.2701446024 0.3646549428 0.0705429973
[31] 0.3528494205 0.5708427052 -0.1422101365 -0.0119632714 -0.5814201140
[36] -0.2701661041 -0.2572632146 -0.4072332874 -0.0938265049 -0.4254094116
[41] -0.3428352572 -0.4033215081 0.0438486530 -0.4105565585 -0.5021043042
[46] -0.5227729336 0.5325813174 -0.3295811829 0.2674977624 0.2704603063
[51] 0.4146452954 -0.2560076683 -0.0903220967 0.2704319623 -0.5722821171
[56] -0.3398610860 0.1179963059 -0.0050245482 -0.5729427667 0.1350019171
[61] -0.2930100207 -0.0113440248 0.7343566233 -0.2035107847 -0.2021817835
[66] 0.2169086236 0.2264823099 -0.5530584874 -0.1819797870 0.3981512352
[71] -0.8173936399 0.0518915006 -0.2287115571 0.0631910548 0.1188361989
[76] 0.2561737106 0.1163119624 0.0635341801 0.2618737448 -0.1658804075
[81] -0.3211075263 0.2780369204 -0.3051016321 -0.1058006778 -0.0258018831
[86] -0.5941105297 0.1645773040 -0.5100977384 0.1603919543 -0.3567824556
[91] -0.0337684788 0.6028010586 0.6624869745 -0.4551780486 -0.5402033319
[96] 0.3141454300 0.2028909846 -0.0684980264 0.0517161825 0.1195163485
[101] -0.0647983003 -0.2215580106 0.4025328355 -0.8946081767 0.2002396804
[106] 0.6784967261 -0.1990044381 -0.2998079190 0.3443257394 -0.2893433011
[111] -0.6328615683 -0.0257975521 -0.3948298356 -0.0933491291 0.0414941184
[116] -0.0672365352 -0.2493523019 -0.2744946410 0.0249831109 -0.8077988107
[121] 0.2449294766 0.0656736654 0.0227586656 0.0706678654 -0.5739548903
[126] -0.0647622224 0.3140097066 -0.5942563414 0.1552122350 0.1714062147
[131] 0.0770406296 0.1483338736 0.5600684615 0.1863641463 0.0423229589
[136] -0.2575704927 0.1104495084 0.3719943334 -0.0543971401 0.2538948917
[141] -0.0829508199 0.1360388598 -0.0411222545 -0.0831697167 -0.2349698572
[146] -0.0973970654 -0.2757215540 0.5843628791 -0.0521620540 -0.1274227695
[151] 0.1315943044 -0.1134708515 -0.6692863556 0.2699620934 0.3755830788
[156] -0.0006221325 -0.3916688748 0.1973366824 -0.0863904695 -0.7150075819
[161] 0.2355639539 -0.4204110857 0.0646691327 -0.2233863368 0.0083413230
[166] 0.0274767811 -0.2940353751 0.0895900547 -0.5351700216 0.2068976917
[171] -0.0300367655 -0.1843699394 0.3573142018 0.0350469219 -0.3724193268
[176] -0.4398842117 -0.3390223639 0.1476192663 -0.1823023992 0.4161045774
[181] 0.3276325104 0.3081994706 0.2192162922 0.0383247040 -0.0607808077
[186] -0.1130195980 -0.3348625715 -0.4949389553 0.6616712326 -0.4660289845
[191] -0.1780149280 -0.1023674857 -0.5729267821 -0.3443731866 -0.2311779642
[196] -0.3762014075 0.7434864088 0.1554210268 -0.3769321399 -0.5151407311
[201] -0.2014132751 -0.2989350555 0.1023069742 -0.1956866857 -0.1278108019
[206] -0.0605221332 0.1179018427 -0.1005354327 0.3578786683 0.1431595018
[211] -0.0927496801 0.0599204950 0.4052862475 -0.0110017714 -0.3408477805
[216] 0.5525887727 -0.2887045469 -0.2664475865 -0.3572204742 0.1300545335
[221] -0.1485353726 -0.1801110601 -0.1578721429 0.0504920045 0.1748592715
[226] -0.2887727023 -0.1317226969 0.2754690414 -0.2577232808 -0.0525704383
>
> proc.time()
user system elapsed
1.266 0.636 1.891
BufferedMatrix.Rcheck/tests/rawCalltesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> prefix <- "dbmtest"
> directory <- getwd()
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x56a41e1411c0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x56a41e1411c0>
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x56a41e1411c0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 10
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000 0.000000 0.000000 0.000000 0.000000 0.000000
1.000000 2.000000 3.000000 4.000000 5.000000 0.000000 0.000000 0.000000 0.000000 0.000000
2.000000 3.000000 4.000000 5.000000 6.000000 0.000000 0.000000 0.000000 0.000000 0.000000
3.000000 4.000000 5.000000 6.000000 7.000000 0.000000 0.000000 0.000000 0.000000 0.000000
4.000000 5.000000 6.000000 7.000000 8.000000 0.000000 0.000000 0.000000 0.000000 0.000000
<pointer: 0x56a41e1411c0>
> rm(P)
>
> #P <- .Call("R_bm_Destroy",P)
> #.Call("R_bm_Destroy",P)
> #.Call("R_bm_Test_C",P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 0
Buffer Rows: 1
Buffer Cols: 1
Printing Values
<pointer: 0x56a41e424120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x56a41e424120>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 1
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000
0.000000
0.000000
0.000000
0.000000
<pointer: 0x56a41e424120>
> .Call("R_bm_AddColumn",P)
<pointer: 0x56a41e424120>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x56a41e424120>
> rm(P)
>
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,5)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x56a41d0d84a0>
> .Call("R_bm_AddColumn",P)
<pointer: 0x56a41d0d84a0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x56a41d0d84a0>
>
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x56a41d0d84a0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x56a41d0d84a0>
>
> .Call("R_bm_RowMode",P)
<pointer: 0x56a41d0d84a0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x56a41d0d84a0>
>
> .Call("R_bm_ColMode",P)
<pointer: 0x56a41d0d84a0>
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 2
Buffer Rows: 5
Buffer Cols: 5
Printing Values
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
0.000000 0.000000
<pointer: 0x56a41d0d84a0>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x56a41d174390>
> .Call("R_bm_SetPrefix",P,"BufferedMatrixFile")
<pointer: 0x56a41d174390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x56a41d174390>
> .Call("R_bm_AddColumn",P)
<pointer: 0x56a41d174390>
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile98afb5c728306" "BufferedMatrixFile98afb7f22796f"
> rm(P)
> dir(pattern="BufferedMatrixFile")
[1] "BufferedMatrixFile98afb5c728306" "BufferedMatrixFile98afb7f22796f"
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x56a41d9f3650>
> .Call("R_bm_AddColumn",P)
<pointer: 0x56a41d9f3650>
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x56a41d9f3650>
> .Call("R_bm_isReadOnlyMode",P)
[1] TRUE
> .Call("R_bm_ReadOnlyModeToggle",P)
<pointer: 0x56a41d9f3650>
> .Call("R_bm_isReadOnlyMode",P)
[1] FALSE
> .Call("R_bm_isRowMode",P)
[1] FALSE
> .Call("R_bm_RowMode",P)
<pointer: 0x56a41d9f3650>
> .Call("R_bm_isRowMode",P)
[1] TRUE
> .Call("R_bm_ColMode",P)
<pointer: 0x56a41d9f3650>
> .Call("R_bm_isRowMode",P)
[1] FALSE
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_setRows",P,10)
[1] TRUE
> .Call("R_bm_AddColumn",P)
<pointer: 0x56a41eb7a430>
> .Call("R_bm_AddColumn",P)
<pointer: 0x56a41eb7a430>
>
> .Call("R_bm_getSize",P)
[1] 10 2
> .Call("R_bm_getBufferSize",P)
[1] 1 1
> .Call("R_bm_ResizeBuffer",P,5,5)
<pointer: 0x56a41eb7a430>
>
> .Call("R_bm_getBufferSize",P)
[1] 5 5
> .Call("R_bm_ResizeBuffer",P,-1,5)
<pointer: 0x56a41eb7a430>
> rm(P)
>
>
> P <- .Call("R_bm_Create",prefix,directory,1,1)
> .Call("R_bm_Test_C",P)
RBufferedMatrix
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Assigning Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 6.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x56a41ee6f250>
> .Call("R_bm_getValue",P,3,3)
[1] 6
>
> .Call("R_bm_getValue",P,100000,10000)
[1] NA
> .Call("R_bm_setValue",P,3,3,12345.0)
[1] TRUE
> .Call("R_bm_Test_C2",P)
Checking dimensions
Rows: 5
Cols: 5
Buffer Rows: 1
Buffer Cols: 1
Printing Values
0.000000 1.000000 2.000000 3.000000 4.000000
1.000000 2.000000 3.000000 4.000000 5.000000
2.000000 3.000000 4.000000 5.000000 6.000000
3.000000 4.000000 5.000000 12345.000000 7.000000
4.000000 5.000000 6.000000 7.000000 8.000000
<pointer: 0x56a41ee6f250>
> rm(P)
>
> proc.time()
user system elapsed
0.256 0.046 0.290
BufferedMatrix.Rcheck/tests/Rcodetesting.Rout
R version 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"
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> library(BufferedMatrix);library.dynam("BufferedMatrix","BufferedMatrix", .libPaths());
Attaching package: 'BufferedMatrix'
The following objects are masked from 'package:base':
colMeans, colSums, rowMeans, rowSums
>
> Temp <- createBufferedMatrix(100)
> dim(Temp)
[1] 100 0
> buffer.dim(Temp)
[1] 1 1
>
>
> proc.time()
user system elapsed
0.238 0.048 0.273